The Prequel Yodas (I think the Phantom Menace one was actually a puppet) were of far poorer design than the old trilogy's Yoda. Not only did they look less real, but the facial features had a far poorer design. The look on the old Yoda's face was wise an intelligent and benevolent. The Phantom Menace Yoda just looked silly and the later Yoda had this annoying look on his face and they even tried to have him put on macho tough guy expressions, which looked ridiculous. Yoda's lightsaber duels were seriously painful. Here's this little thing zipping around the air buzzing -it was like he was a big fly. It erased what dignity the character had in the prequels (which was far less than he had in the old films, anyway). A poster above said he shouldn't have had to even resort to lightsaber work and I agree. Yoda should have been above such things. He should have used alternatives based on greater mastery of the force. This is one of many examples of bad judgement in the prequels.
Also, it's clear looking at the later Yodas that not enough effort was put in to make the prequel version look like the old version, to make him look like like he was the same guy. Particularly the Phantom Menace version. Why? Surely it couldn't have been so hard to make him look similar. There was some excuse made to the effect that he would have looked different because he was younger, but the Phantom Menace Yoda in particular had totally different features and could never have been the same guy, at any age. The ROTS/AOTC version didn't match up either, and, most importantly, looked like he had a totally different (and far less impressive) personality than the original.
They also wrote Yoda less well in the prequels. He's an annoying pain in the ass there.
Re the lack of realistic appearance of the later Yoda's (the Phantom Menace version looked like a puppet while the later version looked like a cartoon) compared to the splendid old puppet, isn't it amazing how 20 years later they put out something so inferior to what was managed back in the early 80s?
Also, similar to the Yoda situation is the Jabba situation. ROTJ's Jabba is spectacular, lifelike and full of personality. Later Jabbas don't look real, don't have the personality and don't look like any effort was put in to make them look like the same guy as ROTJ's Jabba. And the awful cutsey 1997 Jabba was horrific.